GENEALOGY-DNA-L Archives
Archiver > GENEALOGY-DNA > 2006-03 > 1142274313
From: "Ian & Mary Logan" <>
Subject: Re: [DNA] Uploading a complete mitochondrial sequence to NCBI GenBank, and why this is so useful for the genetic genealogist.
Date: Mon, 13 Mar 2006 18:25:13 -0000
References: <2fc.69ead0.3145a59b@aol.com>
Ted
I have been away for the weekend and have got back to find your long posting
- which I have found to be very interesting.
Last week I submitted a posting announcing the arrival of your NCBI GENBANK
sequence. Giving the details as:
.........
DQ377992(Ashkenazi Jew); submitted by Kandell, T.E. & Greenspan, B.
The sequence mutation list is:
A263G 315.C A750G A1438G A2706G A3397G A4769G
C7028T A8860G C12133T A13105G A15326G
..............
and I am very pleased to see that you have chosen to give the list the background information
to the process of getting your sequence published. The sequence is available at:
http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=88942033
I hope that FTDNA will now get more of their sequences published; and it would be
good if they were to give the option of publication to all their clients.
However, there are just a few points to be discussed.
Firstly, I would suggest the sequences should be anonymous. I see you have chosen
not to do so - but as a rule NCBI Genbank sequences cannot be traced just from
the information given.
Secondly; do we know how FTDNA produced your sequence for publication ?
By this I mean did they work out the mutations (as given above) and then produce
a sequence (an error-prone method), or did they give you the raw sequence as
they produced it ?
And, thirdly:
You might ask FTDNA is they are happy with their program for producing the entry
for NCBI Genbank.
Especially, at the point of the CRS having the 3106 deletion (or 3107 if you are fussy)
and their decision not to mark this in your sequence. This results in your sequence
being short by 1 nucleotide - as compared to the usual convention.
Also, I have only checked the tRNAs, - but I think the CRS gives
tRNA - Ser (UCN) at 7446-7514 & tRNA - Pro at 15956-16023,
and not as given by FTDNA.
I shall be pleased to help in any way possible; and please let us know what FTDNA
has to say.
Ian
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